Yamanaka Factors and Partial Cellular Reprogramming
Today, we chronicle the progress of partial cellular reprogramming and discuss how this powerful technique may be able to reprogram cells back into a youthful state, at least partially reversing epigenetic alterations, one of the proposed reasons we age.
The Yamanaka factors and the birth of partial cellular reprogramming
In 2006, a study by Drs. Kazutoshi and Shinya Yamanaka showed that it was possible to reprogram cells using just four master genes named Oct4, Sox2, Klf4, and c-Myc, or OSKM for short . These four reprogramming factors are often called the Yamanaka factors after one of their discoverers.
Prior to this, it was assumed that egg cells (oocytes) would contain a complex array of factors needed to reprogram a somatic cell into becoming an embryonic cell. After all, the feat of transforming an aged egg cell and reprogramming it to make a new animal must be controlled by many factors present in the egg cell, or so they thought. Takahashi and Yamanaka turned this idea upside down when they showed that just four of the Yamanaka factors were needed to achieve this transformation.
They used the Yamanaka factors to reprogram adult mouse fibroblasts (connective tissue cells) back to an embryonic state called pluripotency, a state where the cell behaves like an embryonic stem cell and can become any other cell type in the body.
This discovery paved the way for research into how these Yamanaka factors might be used for cellular rejuvenation and a potential way to combat age-related diseases.
Yamanaka factors for cellular and animal rejuvenation
In 2011, a team of French researchers, including Jean-Marc Lemaitre, first reported cellular rejuvenation using the Yamanaka factors . During their life, cells express different patterns of genes, and those patterns are unique to each phase in a cell’s life from young to old; this gene expression profile makes it easy to identify an old or young cell. At the time, it was also known that aged cells such as fibroblasts have short telomeres and dysfunctional mitochondria, two of the nine reasons we age .
Jean-Marc Lemaitre and his colleagues tested the effects of Yamanaka factors on aged fibroblasts from normal old people and also from healthy people over 100 years old. They added two additional pluripotency genetic factors to the OSKM mix, namely NANOG and LIN28, and examined the effect that this had on the gene expression, telomeres, and mitochondria of these older people.
They discovered that together, the six factors were able to reset cells from old donors back into a pluripotent state, meaning that they could become any other cell type in the body. These became known as induced pluripotent stem cells (iPSCs).
The researchers noted that the cells had a higher growth rate than the aged cells they had been reprogrammed from; they also had longer telomeres as well as mitochondria that behaved in a youthful manner and were no longer dysfunctional. In other words, reprogramming the cells reversed some of the aspects of aging and rolled the cells back to a similar state as during development.
Yamanaka factors appear to reverse epigenetic aging
The final step for the researchers was to then guide these iPSCs to become fibroblasts again using other reprogramming factors. The result was that these reprogrammed fibroblasts no longer expressed the gene patterns associated with aged cells and had a gene expression profile indistinguishable from those of young fibroblasts. Essentially, they showed that epigenetic alterations (changes to gene expression patterns), a reason we age, were reversed.
In addition to this, they also showed that telomere length, mitochondrial function, and oxidative stress levels had all reset to those typically observed in young fibroblasts. Telomere attrition and mitochondrial dysfunction are two more reasons that we are thought to age.
This was the first evidence that aged cells, even from very old individuals, could be rejuvenated, and this was followed by a flood of independent studies confirming these findings in the same and other types of cells.
Can Yamanaka factors be used in living animals?
It was easy to isolate cells in a dish, take them back to a developmental state, then guide them to become whatever cell type they wanted using Yamanaka factors. But this was obviously not practical in a living animal as cells could not have their memory erased so they reverted to a pluripotent state. Imagine if a heart cell forgot it was a heart cell while it was supposed to be helping pump blood around the body!
There was also the concern that the expression of Yamanaka factors was known to induce cancer in animals .
Some researchers believed that it might be possible to avoid cancer and reverse aging in old cells without completely reverting them to pluripotency. In other words they thought there was a way for us to have our cake and eat it. But no one had successfully managed to achieve this in living animals. This was all about to change in December 2016.
Professor Juan Carlos Izpisua Belmonte and his team of researchers at the Salk Institute reported the conclusion of their study, which showed for the first time that the cells and organs of a living animal could be rejuvenated .
For the study, the researchers used a specially engineered progeric mouse designed to age more rapidly than normal as well as an engineered normally aging mouse strain. Both types of mice were engineered to express the Yamanaka factors when they came into contact with the antibiotic doxycycline, which was given to them via their drinking water.
They allowed the Yamanaka factors to be transiently expressed by including doxycycline in the water for two days then removed it so that the OSKM genes were silenced again. The mice then had a five-day rest period before another two days of exposure to doxycycline; this cycle was repeated for the duration of the study.
Partial cellular reprogramming
After just six weeks of this treatment, which steadily reprogrammed the cells of the mice, the researchers noticed improvements in their appearance, including reduced age-related spinal curvature. Some of the mice from both experiment and control groups were also euthanized at this point so that their skin, kidneys, stomachs, and spleens could be examined. The control mice showed a range of age-related changes compared to the treated mice, which had a number of aging signs halted or even reversed, including some epigenetic alterations.
The treated mice also experienced a 50% increase in their mean survival time in comparison to untreated progeric control mice. It should be noted that not all aging signs were affected by partial cellular reprogramming, and if treatment was halted, the aging signs returned.
Perhaps most importantly, while the partial cellular reprogramming conducted in this periodic manner reset some epigenetic aging signs, it did not reset cell differentiation, which would cause the cell to revert to an embryonic state and forget what kind of cell it previously was; as you can imagine, this would be a bad thing in a living animal.
Finally, not only did the transient expression of Yamanaka factors at least partially rejuvenate cells and organs in progeric mice, but it also appeared to improve tissue regeneration in the engineered 12-month-old normally aging mouse group. The researchers observed that the partial reprogramming improved these mice’s ability to regenerate tissue in the pancreas, resulting in an increased proliferation of beta cells; additionally, there was an increase of satellite cells in skeletal muscle. Both of these types of cells typically decline during aging.
Yamanaka factors used to improve cognitive function in old mice
In October 2020, another study took us a step close to partial cellular reprogramming reaching the clinic when researchers showed that partial cellular reprogramming improves memory in old mice. As the previous studies have shown, partial cellular reprogramming is a balancing act between epigenetically rejuvenating cells and resetting their aging clocks, without completely resetting their cell identity so they forget what kind of cell they are .
Previous studies have also shown us that this balancing act is possible and that by exposing cells just long enough to the reprogramming factors, rejuvenation of the cell is possible without erasing its cellular identity.
As in the previous study we talked about, mice in this study had their cells engineered to react to doxycycline, a common antibiotic used in veterinary practice, in order to express the OSKM reprogramming factors. The researchers found that giving the mice just enough exposure improved their cognitive function without an increase in mortality during a four-month period.
Another step forward for partial cellular reprogramming
In late 2020, researchers, including Dr. David Sinclair, published a study that showed that they had managed to restore lost vision to old mice, and mice with damaged retinal nerves, using partial cellular reprogramming .
To reduce cancer risk they opted to try partial cellular reprogramming minus one of the Yamanaka Factors. One of the study authors, Dr. Yuancheng Lu, was looking for a safer way to rejuvenate aged cells, as there were some concerns that using c-Myc could cause cancer under certain circumstances. So in the end they opted to use just Oct4, Sox2, and Klf4 (OSK).
The good news was that even OSK was able to rejuvenate the damaged eye nerves in mice and restore vision. It also worked to improve age-related vision impairment in treated mice and in mice that experienced increased eye pressure, an emulation of glaucoma.
Study co-author, Dr. David Sinclair, said in an article in Nature, “We set out with a question: if epigenetic changes are a driver of ageing, can you reset the epigenome?”, or, in other words, “Can you reverse the clock?”. The answer to that appears to be a resounding yes!
Refining the partial cellular reprogramming method
In January 2021 researchers showed that partial reprogramming rejuvenates human cells by 30 years, making old worn out cells function like the cells of a person around 25 years old. The researchers of this study used an approach that exposed cells to enough reprogramming factors to push them beyond the limit at which they were considered somatic rather than stem cells – but only just beyond .
The fibroblasts that were reprogrammed in this way retained enough of their epigenetic cellular memories to return to being fibroblasts once again. Exposing these cells to the OSKM factors was performed with a doxycycline-activated lentiviral package as previous animal studies had also done.
Perhaps most interesting, according to Horvath’s 2013 multi-tissue clock, sample cells that were just under 60 years old became epigenetically equivalent to cells that were approximately 25 years old after 13 days of partial cellular reprogramming, and the Horvath 2018 skin and blood clock showed that cells that were approximately 40 years old were also epigenetically returned to those of a 25-year-old. It seems that the cells revert an epigenetic age of 25 or so suggesting this is a peak of cellular prime or the optimal functional age for cells.
The challenges ahead for partial cellular reprogramming
By far, the biggest hurdle to translating partial cellular reprogramming to people is the need to find a way to activate the Yamanaka factors in our cells without needing to engineer our bodies to react to a drug such as doxycycline. Doing this may require us to develop drugs capable of activating OSKM, editing every cell in our body to respond to a particular compound like doxycycline, which would be extremely challenging though plausible.
Another possibility is editing the germline so that our children are born with such a modification to respond to a chosen compound, an idea that is currently an ethical nightmare to even consider, not to mention the technical challenges of doing so successfully. Whatever the solution is, it needs to be practical.
The other major hurdle is to find a method suitable for the long term that does not require constant upkeep, lest the aging signs return rapidly, as they did in mice when treatment was interrupted. While there is some reason to believe that these signs would not return as rapidly in people given the differences between mouse and human metabolisms and our superior repair systems, it would likely return in due course. So, finding a cost-effective way to keep the cyclic treatment going is paramount; this could potentially be achieved using drugs or transient gene therapy.
The future of Yamanaka factors to combat Aging
Assuming that these barriers can be overcome, and the rapid advances in biotechnology offer a reason to think that they will, then partial cellular reprogramming could feasibly hold a great deal of potential for preventing or even curing the diseases of aging.
One might envision an early, first-pass use of this approach in a preventative way: older people at risk of age-related diseases could be given partial reprogramming in order to halt or at the least significantly slow down this aspect of aging and thus reduce their risk of developing age-related diseases.
More refined stages may see it being used in a more focused manner to repair a certain organ or tissue damaged by injury or disease. In another, more advanced, scenario, the gradual whole-body rejuvenation of older people might be attempted in order to totally prevent age-related diseases and keep them healthy, active and able to continue enjoying life.
Companies such as Google Calico are also currently investigating alternative ways to achieve partial cellular reprogramming without using Yamanaka factors. This is another direction of research that may prove more practical and safer than using Yamanaka factors.
The rapid progress of medical technology could potentially mean that such partial cellular reprogramming therapies may become available in the not too distant future. We certainly hope so.
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